gnomAD MCP Server

Instructions

Implementation Reference

• src/index.ts:708-719 (handler)

  Handler logic for the 'get_coverage' tool within the CallToolRequestSchema handler's switch statement. It validates input, makes a GraphQL request to fetch coverage data, and formats the result.

  case "get_coverage":
    if (!args.gene_id && !args.gene_symbol) {
      throw new Error("Either gene_id or gene_symbol must be provided");
    }
    result = await makeGraphQLRequest(QUERIES.getCoverage, {
      geneId: (args.gene_id as string) || null,
      geneSymbol: (args.gene_symbol as string) || null,
      datasetId: parseDatasetId((args.dataset as string) || "gnomad_r4"),
      referenceGenome: parseReferenceGenome((args.reference_genome as string) || "GRCh38"),
    });
    formattedResult = result.data?.gene?.coverage || null;
    break;

• src/index.ts:558-584 (registration)

  Registration of the 'get_coverage' tool in the ListToolsRequestSchema handler, including name, description, and input schema.

  {
    name: "get_coverage",
    description: "Get coverage information for a gene",
    inputSchema: {
      type: "object",
      properties: {
        gene_id: {
          type: "string",
          description: "Ensembl gene ID",
        },
        gene_symbol: {
          type: "string",
          description: "Gene symbol",
        },
        dataset: {
          type: "string",
          description: "Dataset ID",
          default: "gnomad_r4",
        },
        reference_genome: {
          type: "string",
          description: "Reference genome",
          default: "GRCh38",
        },
      },
    },
  },

• src/index.ts:282-317 (schema)

  GraphQL query schema for fetching gene coverage data, defined in the QUERIES object and used by the handler.

  getCoverage: `
    query GetCoverage($geneId: String, $geneSymbol: String, $datasetId: DatasetId!, $referenceGenome: ReferenceGenomeId!) {
      gene(gene_id: $geneId, gene_symbol: $geneSymbol, reference_genome: $referenceGenome) {
        coverage(dataset: $datasetId) {
          exome {
            pos
            mean
            median
            over_1
            over_5
            over_10
            over_15
            over_20
            over_25
            over_30
            over_50
            over_100
          }
          genome {
            pos
            mean
            median
            over_1
            over_5
            over_10
            over_15
            over_20
            over_25
            over_30
            over_50
            over_100
          }
        }
      }
    }
  `,

• src/index.ts:44-61 (helper)

  Helper function used by the get_coverage handler to execute GraphQL requests to the gnomAD API.

  async function makeGraphQLRequest(query: string, variables: Record<string, any> = {}): Promise<GnomadResponse> {
    const response: Response = await fetch(GNOMAD_API_URL, {
      method: "POST",
      headers: {
        "Content-Type": "application/json",
      },
      body: JSON.stringify({
        query,
        variables,
      }),
    });
  
    if (!response.ok) {
      throw new Error(`HTTP error! status: ${response.status}`);
    }
  
    return await response.json() as GnomadResponse;
  }